Hours after burying his slain cousin, Muhammad Jassem stood in the scorching dirt of a former al-Qaida parade ground speaking about a lurking foe that he knows is hunting him, too.

Nearby, guards waited furtively at the entrance to the Islamic mourning tent for Sheikh Alman al-Shijah, blown apart last Friday by a bomb placed under his car. The rows of plastic seats set up to receive those paying condolences sat mostly empty, melting on the hard-baked plain in the village of al-Qadoon, in Diyala. It was here, Jassem says, that al-Qaida's former leader, Abu Musab al-Zarqawi, would receive cadres.

"I saw him here in 2005," he said. "He was appointing al-Qaida leaders and assigning military roles. This was a difficult neighbourhood – and still is.

"They have tried everything to get us," he added, referring to militants he believes are still doing Zarqawi's bidding. "And they will keep trying. This is still war up here. Our enemy may be cowards, but they are strong."

Sheikh Alman was a leader of the Sons of Iraq, the lauded band of rebels who helped turn the tide of the insurgency from 2006, in many eyes saving Iraq from the abyss. His killers had tried to slay him six times before they finally succeeded. His cousin, Jassem, is also a member. He says he has been the target of 13 would-be hits.

All around the country, Sons of Iraq leaders, also known as members of the Awakening Council, or al-Sahwa, rattle off similar numbers of attempts on their lives with a fatalistic calm. It is hard to find any member operating on the frontlines against Iraq's rejuvenated insurgency who isn't still being regularly threatened by hit squads. Most of their persecutors they claim to know. Many they believe have recently been freed from the now defunct US prison system in Iraq, which at its peak held almost 30,000 detainees. Many others had been rotated through the system during the blood-soaked years of 2006-07. Earlier this year, 15 Awakening members were killed in one night in Abu Ghraib. Things have got a lot worse since.

This week alone, nine members were killed in five days in one of the most lethal weeks the homegrown counter-insurgents have endured. One was slain along with his entire family of five.

Attempts on their lives are becoming such that even battle-hardened leaders, who have known little else but violence for almost five years, are now fearful for themselves and their families.

"I am very worried," said Sheikh Moustafa al-Kamal Shabib, a decorated Awakening Council leader from the south Baghdad suburb of Arab Jabour. From 2005 until early 2008, Sunni insurgents had full rein over the area's farmlands and ran weapons into Baghdad across the Tigris River, which snakes through the area's heart.

Sheikh Moustafa was one of many local leaders the US turned to in 2007 to capitalise on mini-rebellions in Sunni areas against al-Qaida groups which had begun to overplay their hands.

Initially, Iraq's disenfranchised Sunni groups had largely welcomed as reinforcements for a burgeoning resistance the hordes of Arab jihadis who had swarmed across porous borders and sought refuge in places such as Ramadi, Fallujah, west Baghdad and Diyala. But when the guests started imposing sharia law, beheading people on street corners and demanding access to their daughters, hospitality turned into hostility.

"They were wrong and we fought them and killed them by the dozens," said Sheikh Moustafa. The US military locked up hundreds more alleged militants in the Dora neighbourhood of Baghdad alone who had operated with impunity during a total collapse of law and order. "For three years you couldn't drive through here," he said as he pointed out homes flattened by US fighter jets during the surge of 2007.

Militants are not here in the numbers that they were before. But they are active: "Their preferred method is assassination with silencers. But they also put bombs under the cars of leaders."

Like all of Baghdad's 241 remaining Sons of Iraq leaders, Sheikh Moustafa has been given three bodyguards paid for by the Iraqi government. The 1,400-odd foot soldiers who report to him throughout Arab Jabour have been paid $300 (£205) a month by the Iraqi government since the US military handed over responsibility from late-2008 as part of moves to take Iraq to full sovereignty and pave a way for an American exit.

Ever since, it has not been an easy road. The government of prime minister Nouri al-Maliki has had an uneasy relationship with the rebels, who 12 months ago numbered 130,000. Now they are down to 91,405 and within two months of an election result they are set to be no more.

By then, the government aims to integrate all remaining members into government ministries and security forces – budget shortfalls not withstanding.

The Americans came to trust the Awakening Council, with former US commanding general David Petraeus offering amnesties to some leaders.

However, Maliki and his advisers have not felt the same way, fearing the Sons of Iraq are infiltrated by Sunni militants who could use them as a Trojan horse to wreak further terror.

Major general Mudhir al-Mawla, the director of the Sons of Iraq file in Iraq's national reconciliation commission, confirmed the scepticism in the government: "Ever since they began, there have been members of Maliki's administration who oppose them," he said. "They said they are like a militia and they all need to be disarmed. But they have played a very important role in giving precise information because they are locals. They know the locals and they know where their allegiances lie."

In March last year, in a move that underscored the distrust, Maliki's troops arrested a Sons of Iraq leader in the central Baghdad district of Fadhil and a two-day battle ensued. Ever since, he has been reluctant to travel to the frontline areas.

"[Maliki] came here once," said Awakening Council leader Sabah al-Mashadani in what was once another no-go zone in Baghdad, the former battlefield suburb of Adamiyeh. "He was very surprised when he was well received. He said: 'I thought everyone hated me here'."

In Arab Jabour, Sheikh Moustafa has never seen the prime minister, but he has seen his special forces, who arrested the sheikh in January on trumped up charges that he had killed five local men in 2007. The US military quickly took responsibility for the killings and Sheikh Moustafa was released in Maliki's name.

However, the episode underscored the fragility of his position, a feeling he claims is shared by the rank and file. "We are being hunted down. It has never been worse. I have been targeted by roadside bombs six times in the past four months."

Ten days ago, at the back of his family home, a $40,000 pond of fish was poisoned during the night by people he is adamant were linked to al-Qaida. Worse still, Sheikh Moustafa's son spent February in hospital after buying an orange juice that was also laced with poison.

He strongly suspects that he knows who is targeting him. In the village of al-Qadoon, Muhammad Jassem also thinks he knows his family's tormentor.

"That is the benefit of doing what we do," he said. "We know the people and we know where they have been."

In the nearby Diyala police station, Major Hisham al-Jalil, who has locked up most of the area's criminals since 2006, said the spike in attacks was being perpetrated by men who had returned from the US prisons and who blamed the Sons of Iraq for having sent them there.

"They see them as traitors," he said. "They hate the security forces too, but their vengeance is even stronger for the al-Sahwa, some of whom they fought alongside as insurgents. It is only going to get worse here."

With the US military only three months away from having no further combat role in Iraq, the Sons of Iraq are feeling isolated and abandoned. Their legacy will shape the declining months of the seven-year occupation, a fact the US military knows well.

Pressed on the hardships the US-backed rebels are facing, US major general Joseph Reynes, who is responsible for the remaining American side of the Sons of Iraq project, said leaders he spoke to felt they had a national duty to ward off the resurgent militancy.

"I went to Fallujah recently and spoke with a Sahwa leader who said as an Iraqi he must stand his post. They are soldiers on the front lines. This is an insurgency. It's tough. That's why we stand here as brothers moving forward in this fight."

But Sheikh Moustafa feels that brotherhood may fade away as the US withdraws from the bitter battleground of Iraq. "We were there when the Americans wanted us and we have never left," he says. "But there will be no one here for us when the Americans are gone."

From local heroes to al-Qaida's national nemesis

The Sons of Iraq grew out of a series of mini-rebellions against militants associated with al-Qaida that started in late 2006 – first in Anbar province, then spreading to Baghdad and elsewhere in the country.

The initial rebels included those who had been co-opted by al-Qaida, or had willingly offered their services as anti-occupation fighters before realising what that entailed. Al-Qaida were hounded out of Anbar, with American military backing, after over-playing their hand with locals. The then US commander in Iraq, General David Petraeus (pictured), was quick to capitalise on the regional uprisings, which morphed into a nationwide rebellion against al-Qaida.

The US military offered many Sons of Iraq members amnesty and set up a formal programme, which at one stage paid 130,000 members, many of them former insurgents, $300 (£205) each a month.

The Sons of Iraq have been credited with a prominent role in stabilising the country. However, they have struggled to win the trust and full backing of the Shia-majority Iraqi government, which fears the Sons of Iraq ranks have been infiltrated by Sunni militants.

The Iraqi government has pledged to give all members jobs in either the security forces, or government departments. However, as the project winds down, Sons of Iraq members are being hunted down by insurgents who have been freed from US and Iraqi prisons and are determined to avenge old scores.